Degradation of RNA molecules provides a powerful means to control the expression of specific genes. One of the major RNA degradation pathways in eukaryotic cells is the Nonsense-Mediated mRNA decay pathway, which degrades RNA containing premature translation termination codons (PTCs). While the functions of this pathway in eliminating PTC-containing RNAs are well documented, the impact of this pathway in the regulation of expression and the quality control of endogenous transcripts is still unclear. The proposed project will focus on three major functions for NMD in specific gene regulation pathways. First, we will study how NMD can cooperate with other degradation systems to degrade unspliced pre-mRNAs, and the mechanisms that are involved to direct these unspliced RNAs to the different degradation routes. This function is highly critical since accumulation of unspliced pre-mRNAs would result in the production of proteins with deleterious or dominant-negative properties. In addition we will investigate how NMD can regulate the production of alternatively spliced or regulated transcripts. This will include the genomic investigation of transcripts that are spliced at alternative splice sites that include PTCs using RNA-Seq approaches, and understanding how these alternative splicing events are regulated to respond to environmental changes. We have also found an unexpected function for the NMD RNA helicase Upf1p in the control of transcripts specifically spliced or expressed during meiosis and we will investigate the specific role of Upf1p in this process. Finally we found that NMD degrades 5'-extended forms of many genes located within subtelomeric regions, and we have demonstrated that these extended forms mediate the repression of transcription at the bona fide promoters. We will investigate the mechanisms by which these RNAs mediate these repressive functions and the role of NMD in this novel regulatory system. Overall the proposed studies should illustrate the major impact of RNA degradation by NMD in the regulation of gene expression and reveal novel paradigms of gene regulation controlled by this unique RNA quality control pathway. PUBLIC HEALTH RELEVANCE: Mutations that cause genetic diseases often result in premature translation termination codons, which in turn mediate the rapid degradation of mRNAs encoded by these genes by Nonsense Mediated Decay. Genetic Diseases can also result from mutations in splicing signals, which reduce the splicing efficiency or activate cryptic splice sites. Our studies of the turnover of unspliced and mis-spliced RNAs will shed light on the mechanisms by which RNA degradation controls the expression of genes mutated in the context of a large number of genetic diseases.